Van Sowerwine's "Play With Me". Eyes and broken teapot shards. That is all.
Neurotically Yours has an episode called Eye Stigmata, which should tell you a lot. There is also one which has this gem of dialog:
Begley:"I don't recall anyone ever got stuck in the eye with a needle." Pilz-E:"You havn't been to the doctors that I've been to! Needles in the eyes!"
Ninjai The Little Ninja had an epic one... During his escape, Ninjai wounds the Big Bad's eye. The Big Bad, already off in the head and driven further into madness by Ninjai pulls the eye out of his socket and holds it, still connected. He then looks at his own face and then... pops the thing in his mouth, optic nerve intact and eats his own eye. Jesus.
"Eyes Cold Lemonade," where a sign knocks out one of Petunia's eyes and Giggles cuts it in half (thinking it's a lemon) and squeezes the ooze into a cup.
In "Eye Candy," Toothy accidentally knocks one of his eyes out with a lollipop, then ends up hanging from a tree by his nerve and his other eye is pulled out of his head along with his brain. (Pictured above)
In another Nutty gets stabbed in the eye with a spring, Lumpy gets an eye yanked out in "We're Scrooged!", and thinking he's going to kill her Flaky stabs Flippy in the eye with a shard of glass in "Without a Hitch".
In one episode, Flippy gives this to Mime via paper cut. OUCH.
One scene in the Homestar Runner animation "Let us give TANKS!" involved the Blue Laser Commander jabbing a minion in the eye with a giant fork due to him being extremely annoyed by the fact that all of his henchmen look exactly alike.
Casca: Are you a big fan of Nick Fury? Soldier: Well, yeah, he's a total badass. Why? Casca: Ohhh, no reason... Soldier: Ow! My eye! I'm not supposed to get sharp pieces of wood in it! My doctor said so!
And when you thought that part was bad.
Soldier: Well, at least I have the other one *takes a dagger to the remaining eye* oh now this is re-GODDAMN-diculous!